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Dec 11

MLAgentBench: Evaluating Language Agents on Machine Learning Experimentation

A central aspect of machine learning research is experimentation, the process of designing and running experiments, analyzing the results, and iterating towards some positive outcome (e.g., improving accuracy). Could agents driven by powerful language models perform machine learning experimentation effectively? To answer this question, we introduce MLAgentBench, a suite of 13 tasks ranging from improving model performance on CIFAR-10 to recent research problems like BabyLM. For each task, an agent can perform actions like reading/writing files, executing code, and inspecting outputs. We then construct an agent that can perform ML experimentation based on ReAct framework. We benchmark agents based on Claude v1.0, Claude v2.1, Claude v3 Opus, GPT-4, GPT-4-turbo, Gemini-Pro, and Mixtral and find that a Claude v3 Opus agent is the best in terms of success rate. It can build compelling ML models over many tasks in MLAgentBench with 37.5% average success rate. Our agents also display highly interpretable plans and actions. However, the success rates vary considerably; they span from 100% on well-established older datasets to as low as 0% on recent Kaggle challenges created potentially after the underlying LM was trained. Finally, we identify several key challenges for LM-based agents such as long-term planning and reducing hallucination. Our code is released at https://github.com/snap-stanford/MLAgentBench.

  • 4 authors
·
Oct 5, 2023

MLE-Dojo: Interactive Environments for Empowering LLM Agents in Machine Learning Engineering

We introduce MLE-Dojo, a Gym-style framework for systematically reinforcement learning, evaluating, and improving autonomous large language model (LLM) agents in iterative machine learning engineering (MLE) workflows. Unlike existing benchmarks that primarily rely on static datasets or single-attempt evaluations, MLE-Dojo provides an interactive environment enabling agents to iteratively experiment, debug, and refine solutions through structured feedback loops. Built upon 200+ real-world Kaggle challenges, MLE-Dojo covers diverse, open-ended MLE tasks carefully curated to reflect realistic engineering scenarios such as data processing, architecture search, hyperparameter tuning, and code debugging. Its fully executable environment supports comprehensive agent training via both supervised fine-tuning and reinforcement learning, facilitating iterative experimentation, realistic data sampling, and real-time outcome verification. Extensive evaluations of eight frontier LLMs reveal that while current models achieve meaningful iterative improvements, they still exhibit significant limitations in autonomously generating long-horizon solutions and efficiently resolving complex errors. Furthermore, MLE-Dojo's flexible and extensible architecture seamlessly integrates diverse data sources, tools, and evaluation protocols, uniquely enabling model-based agent tuning and promoting interoperability, scalability, and reproducibility. We open-source our framework and benchmarks to foster community-driven innovation towards next-generation MLE agents.

  • 11 authors
·
May 12 2

Benchmarking On-Device Machine Learning on Apple Silicon with MLX

The recent widespread adoption of Large Language Models (LLMs) and machine learning in general has sparked research interest in exploring the possibilities of deploying these models on smaller devices such as laptops and mobile phones. This creates a need for frameworks and approaches that are capable of taking advantage of on-device hardware. The MLX framework was created to address this need. It is a framework optimized for machine learning (ML) computations on Apple silicon devices, facilitating easier research, experimentation, and prototyping. This paper presents a performance evaluation of MLX, focusing on inference latency of transformer models. We compare the performance of different transformer architecture implementations in MLX with their Pytorch counterparts. For this research we create a framework called MLX-transformers which includes different transformer implementations in MLX and downloads the model checkpoints in pytorch and converts it to the MLX format. By leveraging the advanced architecture and capabilities of Apple Silicon, MLX-Transformers enables seamless execution of transformer models directly sourced from Hugging Face, eliminating the need for checkpoint conversion often required when porting models between frameworks. Our study benchmarks different transformer models on two Apple Silicon macbook devices against an NVIDIA CUDA GPU. Specifically, we compare the inference latency performance of models with the same parameter sizes and checkpoints. We evaluate the performance of BERT, RoBERTa, and XLM-RoBERTa models, with the intention of extending future work to include models of different modalities, thus providing a more comprehensive assessment of MLX's capabilities. The results highlight MLX's potential in enabling efficient and more accessible on-device ML applications within Apple's ecosystem.

  • 2 authors
·
Oct 21

An inorganic ABX3 perovskite materials dataset for target property prediction and classification using machine learning

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

  • 2 authors
·
Dec 18, 2023

Grad DFT: a software library for machine learning enhanced density functional theory

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT; an endeavor with many open questions and technical challenges. In this work, we present Grad DFT: a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. Grad DFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, Grad DFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

  • 5 authors
·
Sep 22, 2023

MLR-Bench: Evaluating AI Agents on Open-Ended Machine Learning Research

Recent advancements in AI agents have demonstrated their growing potential to drive and support scientific discovery. In this work, we introduce MLR-Bench, a comprehensive benchmark for evaluating AI agents on open-ended machine learning research. MLR-Bench includes three key components: (1) 201 research tasks sourced from NeurIPS, ICLR, and ICML workshops covering diverse ML topics; (2) MLR-Judge, an automated evaluation framework combining LLM-based reviewers with carefully designed review rubrics to assess research quality; and (3) MLR-Agent, a modular agent scaffold capable of completing research tasks through four stages: idea generation, proposal formulation, experimentation, and paper writing. Our framework supports both stepwise assessment across these distinct research stages, and end-to-end evaluation of the final research paper. We then use MLR-Bench to evaluate six frontier LLMs and an advanced coding agent, finding that while LLMs are effective at generating coherent ideas and well-structured papers, current coding agents frequently (e.g., in 80% of the cases) produce fabricated or invalidated experimental results--posing a major barrier to scientific reliability. We validate MLR-Judge through human evaluation, showing high agreement with expert reviewers, supporting its potential as a scalable tool for research evaluation. We open-source MLR-Bench to help the community benchmark, diagnose, and improve AI research agents toward trustworthy and transparent scientific discovery.

  • 10 authors
·
May 26 1

AIssistant: An Agentic Approach for Human--AI Collaborative Scientific Work on Reviews and Perspectives in Machine Learning

Advances in AI-assisted research have introduced powerful tools for literature retrieval, hypothesis generation, experimentation, and manuscript preparation. However, systems remain fragmented and lack human-centred workflows. To address these gaps, we introduce AIssistant, an agentic, open-source Human-AI collaborative framework designed to simplify the end-to-end creation of scientific workflows. Since our development is still in an early stage, we present here the first experiments with AIssistant for perspective and review research papers in machine learning. Our system integrates modular tools and agents for literature synthesis, section-wise experimentation, citation management, and automatic LaTeX paper text generation, while maintaining human oversight at every stage to ensure accuracy, coherence, and scholarly rigour. We conducted a comprehensive evaluation across three layers: (1) Independent Human Review, following NeurIPS double-blind standards; (2) Automated LLM Review, using GPT-5 as a scalable human review proxy; and (3) Program Chair Oversight, where the chair monitors the entire review process and makes final validation and acceptance decisions. The results demonstrate that AIssistant improves drafting efficiency and thematic consistency. Nonetheless, Human-AI collaboration remains essential for maintaining factual correctness, methodological soundness, and ethical compliance. Despite its effectiveness, we identify key limitations, including hallucinated citations, difficulty adapting to dynamic paper structures, and incomplete integration of multimodal content.

  • 4 authors
·
Sep 14

Towards Provably Unlearnable Examples via Bayes Error Optimisation

The recent success of machine learning models, especially large-scale classifiers and language models, relies heavily on training with massive data. These data are often collected from online sources. This raises serious concerns about the protection of user data, as individuals may not have given consent for their data to be used in training. To address this concern, recent studies introduce the concept of unlearnable examples, i.e., data instances that appear natural but are intentionally altered to prevent models from effectively learning from them. While existing methods demonstrate empirical effectiveness, they typically rely on heuristic trials and lack formal guarantees. Besides, when unlearnable examples are mixed with clean data, as is often the case in practice, their unlearnability disappears. In this work, we propose a novel approach to constructing unlearnable examples by systematically maximising the Bayes error, a measurement of irreducible classification error. We develop an optimisation-based approach and provide an efficient solution using projected gradient ascent. Our method provably increases the Bayes error and remains effective when the unlearning examples are mixed with clean samples. Experimental results across multiple datasets and model architectures are consistent with our theoretical analysis and show that our approach can restrict data learnability, effectively in practice.

  • 4 authors
·
Nov 11

MLGym: A New Framework and Benchmark for Advancing AI Research Agents

We introduce Meta MLGym and MLGym-Bench, a new framework and benchmark for evaluating and developing LLM agents on AI research tasks. This is the first Gym environment for machine learning (ML) tasks, enabling research on reinforcement learning (RL) algorithms for training such agents. MLGym-bench consists of 13 diverse and open-ended AI research tasks from diverse domains such as computer vision, natural language processing, reinforcement learning, and game theory. Solving these tasks requires real-world AI research skills such as generating new ideas and hypotheses, creating and processing data, implementing ML methods, training models, running experiments, analyzing the results, and iterating through this process to improve on a given task. We evaluate a number of frontier large language models (LLMs) on our benchmarks such as Claude-3.5-Sonnet, Llama-3.1 405B, GPT-4o, o1-preview, and Gemini-1.5 Pro. Our MLGym framework makes it easy to add new tasks, integrate and evaluate models or agents, generate synthetic data at scale, as well as develop new learning algorithms for training agents on AI research tasks. We find that current frontier models can improve on the given baselines, usually by finding better hyperparameters, but do not generate novel hypotheses, algorithms, architectures, or substantial improvements. We open-source our framework and benchmark to facilitate future research in advancing the AI research capabilities of LLM agents.

Train Once, Answer All: Many Pretraining Experiments for the Cost of One

Recent work has demonstrated that controlled pretraining experiments are a powerful tool for understanding learning, reasoning, and memorization in large language models (LLMs). However, the computational cost of pretraining presents a significant constraint. To overcome this constraint, we propose to conduct multiple pretraining experiments simultaneously during a single training run. We demonstrate the feasibility of this approach by conducting ten experiments during the training of a 1.5B parameter model on 210B tokens. Although we only train a single model, we can replicate the results from multiple previous works on data contamination, poisoning, and memorization. We also conduct novel investigations into knowledge acquisition, mathematical reasoning, and watermarking. For example, we dynamically update the training data until the model acquires a particular piece of knowledge. Remarkably, the influence of the ten experiments on the model's training dynamics and overall performance is minimal. However, interactions between different experiments may act as a potential confounder in our approach. We propose to test for interactions with continual pretraining experiments, finding them to be negligible in our setup. Overall, our findings suggest that performing multiple pretraining experiments in a single training run can enable rigorous scientific experimentation with large models on a compute budget.

  • 2 authors
·
Sep 27

FML-bench: A Benchmark for Automatic ML Research Agents Highlighting the Importance of Exploration Breadth

Large language models (LLMs) have sparked growing interest in automatic machine learning research agents. Among them, agents capable of autonomously proposing ideas and conducting machine learning experiments are particularly promising, as they maximize research automation and accelerate scientific progress by iteratively refining ideas based on experimental results. However, comprehensively evaluating such agents remains challenging. Existing benchmarks tend to overemphasize engineering aspects while neglecting academic rigor, creating barriers that obscure a clear assessment of an agent's scientific capabilities in machine learning research. They also suffer from limited task diversity, an overemphasis on application-oriented tasks over fundamental research problems, and limited scalability to realistic research settings. To address these limitations, we introduce FML-bench, a benchmark designed to evaluate automatic machine learning research agents on 8 diverse and fundamental machine learning research problems. It reduces coding burden, emphasizes fundamental problems rather than specific use cases, offers high task diversity, and is extensible to real-world machine learning GitHub repositories. Furthermore, we present a unified evaluation framework with five complementary metrics, designed to comprehensively assess agent performance on our benchmark. We evaluate state-of-the-art automatic research agents on FML-bench, and find that agents employing broad research exploration strategies outperform those focusing on narrow but deep exploration. These findings suggest that emphasizing the breadth of exploration may lead to more effective research outcomes than focusing solely on incremental refinement. Our benchmark is available at https://github.com/qrzou/FML-bench.

Building a Family of Data Augmentation Models for Low-cost LLM Fine-tuning on the Cloud

Specializing LLMs in various domain-specific tasks has emerged as a critical step towards achieving high performance. However, the construction and annotation of datasets in specific domains are always very costly. Apart from using superior and expensive closed-source LLM APIs to construct datasets, some open-source models have become strong enough to handle dataset construction in many scenarios. Thus, we present a family of data augmentation models designed to significantly improve the efficiency for model fine-tuning. These models, trained based on sufficiently small LLMs, support key functionalities with low inference costs: instruction expansion, instruction refinement, and instruction-response pair expansion. To fulfill this goal, we first construct an automatic data collection system with seed datasets generated from both public repositories and our in-house datasets. This system leverages powerful LLMs to expand, refine and re-write the instructions and responses, incorporating quality assessment techniques. Following this, we introduce the training process of our models, which effectively distills task-solving and text synthesis abilities from teacher LLMs. Finally, we demonstrate how we integrate these functionalities into a machine learning platform to support low-cost LLM fine-tuning from both dataset preparation and training perspectives for users. Experiments and an application study prove the effectiveness of our approach.

  • 4 authors
·
Dec 6, 2024

An Experience Report on Machine Learning Reproducibility: Guidance for Practitioners and TensorFlow Model Garden Contributors

Machine learning techniques are becoming a fundamental tool for scientific and engineering progress. These techniques are applied in contexts as diverse as astronomy and spam filtering. However, correctly applying these techniques requires careful engineering. Much attention has been paid to the technical potential; relatively little attention has been paid to the software engineering process required to bring research-based machine learning techniques into practical utility. Technology companies have supported the engineering community through machine learning frameworks such as TensorFLow and PyTorch, but the details of how to engineer complex machine learning models in these frameworks have remained hidden. To promote best practices within the engineering community, academic institutions and Google have partnered to launch a Special Interest Group on Machine Learning Models (SIGMODELS) whose goal is to develop exemplary implementations of prominent machine learning models in community locations such as the TensorFlow Model Garden (TFMG). The purpose of this report is to define a process for reproducing a state-of-the-art machine learning model at a level of quality suitable for inclusion in the TFMG. We define the engineering process and elaborate on each step, from paper analysis to model release. We report on our experiences implementing the YOLO model family with a team of 26 student researchers, share the tools we developed, and describe the lessons we learned along the way.

  • 10 authors
·
Jul 2, 2021

Towards Exact Computation of Inductive Bias

Much research in machine learning involves finding appropriate inductive biases (e.g. convolutional neural networks, momentum-based optimizers, transformers) to promote generalization on tasks. However, quantification of the amount of inductive bias associated with these architectures and hyperparameters has been limited. We propose a novel method for efficiently computing the inductive bias required for generalization on a task with a fixed training data budget; formally, this corresponds to the amount of information required to specify well-generalizing models within a specific hypothesis space of models. Our approach involves modeling the loss distribution of random hypotheses drawn from a hypothesis space to estimate the required inductive bias for a task relative to these hypotheses. Unlike prior work, our method provides a direct estimate of inductive bias without using bounds and is applicable to diverse hypothesis spaces. Moreover, we derive approximation error bounds for our estimation approach in terms of the number of sampled hypotheses. Consistent with prior results, our empirical results demonstrate that higher dimensional tasks require greater inductive bias. We show that relative to other expressive model classes, neural networks as a model class encode large amounts of inductive bias. Furthermore, our measure quantifies the relative difference in inductive bias between different neural network architectures. Our proposed inductive bias metric provides an information-theoretic interpretation of the benefits of specific model architectures for certain tasks and provides a quantitative guide to developing tasks requiring greater inductive bias, thereby encouraging the development of more powerful inductive biases.

  • 5 authors
·
Jun 22, 2024

Look Before you Leap: Estimating LLM Benchmark Scores from Descriptions

Progress in large language models is constrained by an evaluation bottleneck: build a benchmark, evaluate models and settings, then iterate. We therefore ask a simple question: can we forecast outcomes before running any experiments? We study text-only performance forecasting: estimating a model's score from a redacted task description and intended configuration, with no access to dataset instances. To support systematic study, we curate PRECOG, a corpus of redacted description-performance pairs spanning diverse tasks, domains, and metrics. Experiments show the task is challenging but feasible: models equipped with a retrieval module that excludes source papers achieve moderate prediction performance with well-calibrated uncertainty, reaching mean absolute error as low as 8.7 on the Accuracy subset at high-confidence thresholds. Our analysis indicates that stronger reasoning models engage in diverse, iterative querying, whereas current open-source models lag and often skip retrieval or gather evidence with limited diversity. We further test a zero-leakage setting, forecasting on newly released datasets or experiments before their papers are indexed, where GPT-5 with built-in web search still attains nontrivial prediction accuracy. Overall, our corpus and analyses offer an initial step toward open-ended anticipatory evaluation, supporting difficulty estimation and smarter experiment prioritization.

  • 4 authors
·
Sep 24

DATED: Guidelines for Creating Synthetic Datasets for Engineering Design Applications

Exploiting the recent advancements in artificial intelligence, showcased by ChatGPT and DALL-E, in real-world applications necessitates vast, domain-specific, and publicly accessible datasets. Unfortunately, the scarcity of such datasets poses a significant challenge for researchers aiming to apply these breakthroughs in engineering design. Synthetic datasets emerge as a viable alternative. However, practitioners are often uncertain about generating high-quality datasets that accurately represent real-world data and are suitable for the intended downstream applications. This study aims to fill this knowledge gap by proposing comprehensive guidelines for generating, annotating, and validating synthetic datasets. The trade-offs and methods associated with each of these aspects are elaborated upon. Further, the practical implications of these guidelines are illustrated through the creation of a turbo-compressors dataset. The study underscores the importance of thoughtful sampling methods to ensure the appropriate size, diversity, utility, and realism of a dataset. It also highlights that design diversity does not equate to performance diversity or realism. By employing test sets that represent uniform, real, or task-specific samples, the influence of sample size and sampling strategy is scrutinized. Overall, this paper offers valuable insights for researchers intending to create and publish synthetic datasets for engineering design, thereby paving the way for more effective applications of AI advancements in the field. The code and data for the dataset and methods are made publicly accessible at https://github.com/cyrilpic/radcomp .

  • 3 authors
·
May 15, 2023

Aligning Language Models with Observational Data: Opportunities and Risks from a Causal Perspective

Large language models are being widely used across industries to generate content that contributes directly to key performance metrics, such as conversion rates. Pretrained models, however, often fall short when it comes to aligning with human preferences or optimizing for business objectives. As a result, fine-tuning with good-quality labeled data is essential to guide models to generate content that achieves better results. Controlled experiments, like A/B tests, can provide such data, but they are often expensive and come with significant engineering and logistical challenges. Meanwhile, companies have access to a vast amount of historical (observational) data that remains underutilized. In this work, we study the challenges and opportunities of fine-tuning LLMs using observational data. We show that while observational outcomes can provide valuable supervision, directly fine-tuning models on such data can lead them to learn spurious correlations. We present empirical evidence of this issue using various real-world datasets and propose DeconfoundLM, a method that explicitly removes the effect of known confounders from reward signals. Using simulation experiments, we demonstrate that DeconfoundLM improves the recovery of causal relationships and mitigates failure modes found in fine-tuning methods that ignore or naively incorporate confounding variables. Our findings highlight that while observational data presents risks, with the right causal corrections, it can be a powerful source of signal for LLM alignment. Please refer to the project page for code and related resources.

  • 1 authors
·
May 30

A Deep Learning Framework for Lifelong Machine Learning

Humans can learn a variety of concepts and skills incrementally over the course of their lives while exhibiting many desirable properties, such as continual learning without forgetting, forward transfer and backward transfer of knowledge, and learning a new concept or task with only a few examples. Several lines of machine learning research, such as lifelong machine learning, few-shot learning, and transfer learning attempt to capture these properties. However, most previous approaches can only demonstrate subsets of these properties, often by different complex mechanisms. In this work, we propose a simple yet powerful unified deep learning framework that supports almost all of these properties and approaches through one central mechanism. Experiments on toy examples support our claims. We also draw connections between many peculiarities of human learning (such as memory loss and "rain man") and our framework. As academics, we often lack resources required to build and train, deep neural networks with billions of parameters on hundreds of TPUs. Thus, while our framework is still conceptual, and our experiment results are surely not SOTA, we hope that this unified lifelong learning framework inspires new work towards large-scale experiments and understanding human learning in general. This paper is summarized in two short YouTube videos: https://youtu.be/gCuUyGETbTU (part 1) and https://youtu.be/XsaGI01b-1o (part 2).

  • 2 authors
·
Apr 30, 2021

BoxingGym: Benchmarking Progress in Automated Experimental Design and Model Discovery

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

  • 7 authors
·
Jan 2 2

Model Evaluation, Model Selection, and Algorithm Selection in Machine Learning

The correct use of model evaluation, model selection, and algorithm selection techniques is vital in academic machine learning research as well as in many industrial settings. This article reviews different techniques that can be used for each of these three subtasks and discusses the main advantages and disadvantages of each technique with references to theoretical and empirical studies. Further, recommendations are given to encourage best yet feasible practices in research and applications of machine learning. Common methods such as the holdout method for model evaluation and selection are covered, which are not recommended when working with small datasets. Different flavors of the bootstrap technique are introduced for estimating the uncertainty of performance estimates, as an alternative to confidence intervals via normal approximation if bootstrapping is computationally feasible. Common cross-validation techniques such as leave-one-out cross-validation and k-fold cross-validation are reviewed, the bias-variance trade-off for choosing k is discussed, and practical tips for the optimal choice of k are given based on empirical evidence. Different statistical tests for algorithm comparisons are presented, and strategies for dealing with multiple comparisons such as omnibus tests and multiple-comparison corrections are discussed. Finally, alternative methods for algorithm selection, such as the combined F-test 5x2 cross-validation and nested cross-validation, are recommended for comparing machine learning algorithms when datasets are small.

  • 1 authors
·
Nov 13, 2018

70 years of machine learning in geoscience in review

This review gives an overview of the development of machine learning in geoscience. A thorough analysis of the co-developments of machine learning applications throughout the last 70 years relates the recent enthusiasm for machine learning to developments in geoscience. I explore the shift of kriging towards a mainstream machine learning method and the historic application of neural networks in geoscience, following the general trend of machine learning enthusiasm through the decades. Furthermore, this chapter explores the shift from mathematical fundamentals and knowledge in software development towards skills in model validation, applied statistics, and integrated subject matter expertise. The review is interspersed with code examples to complement the theoretical foundations and illustrate model validation and machine learning explainability for science. The scope of this review includes various shallow machine learning methods, e.g. Decision Trees, Random Forests, Support-Vector Machines, and Gaussian Processes, as well as, deep neural networks, including feed-forward neural networks, convolutional neural networks, recurrent neural networks and generative adversarial networks. Regarding geoscience, the review has a bias towards geophysics but aims to strike a balance with geochemistry, geostatistics, and geology, however excludes remote sensing, as this would exceed the scope. In general, I aim to provide context for the recent enthusiasm surrounding deep learning with respect to research, hardware, and software developments that enable successful application of shallow and deep machine learning in all disciplines of Earth science.

  • 1 authors
·
Jun 16, 2020

Zero-shot and Few-shot Learning with Knowledge Graphs: A Comprehensive Survey

Machine learning especially deep neural networks have achieved great success but many of them often rely on a number of labeled samples for supervision. As sufficient labeled training data are not always ready due to e.g., continuously emerging prediction targets and costly sample annotation in real world applications, machine learning with sample shortage is now being widely investigated. Among all these studies, many prefer to utilize auxiliary information including those in the form of Knowledge Graph (KG) to reduce the reliance on labeled samples. In this survey, we have comprehensively reviewed over 90 papers about KG-aware research for two major sample shortage settings -- zero-shot learning (ZSL) where some classes to be predicted have no labeled samples, and few-shot learning (FSL) where some classes to be predicted have only a small number of labeled samples that are available. We first introduce KGs used in ZSL and FSL as well as their construction methods, and then systematically categorize and summarize KG-aware ZSL and FSL methods, dividing them into different paradigms such as the mapping-based, the data augmentation, the propagation-based and the optimization-based. We next present different applications, including not only KG augmented prediction tasks such as image classification, question answering, text classification and knowledge extraction, but also KG completion tasks, and some typical evaluation resources for each task. We eventually discuss some challenges and open problems from different perspectives.

  • 8 authors
·
Dec 18, 2021

asanAI: In-Browser, No-Code, Offline-First Machine Learning Toolkit

Machine learning (ML) has become crucial in modern life, with growing interest from researchers and the public. Despite its potential, a significant entry barrier prevents widespread adoption, making it challenging for non-experts to understand and implement ML techniques. The increasing desire to leverage ML is counterbalanced by its technical complexity, creating a gap between potential and practical application. This work introduces asanAI, an offline-first, open-source, no-code machine learning toolkit designed for users of all skill levels. It allows individuals to design, debug, train, and test ML models directly in a web browser, eliminating the need for software installations and coding. The toolkit runs on any device with a modern web browser, including smartphones, and ensures user privacy through local computations while utilizing WebGL for enhanced GPU performance. Users can quickly experiment with neural networks and train custom models using various data sources, supported by intuitive visualizations of network structures and data flows. asanAI simplifies the teaching of ML concepts in educational settings and is released under an open-source MIT license, encouraging modifications. It also supports exporting models in industry-ready formats, empowering a diverse range of users to effectively learn and apply machine learning in their projects. The proposed toolkit is successfully utilized by researchers of ScaDS.AI to swiftly draft and test machine learning ideas, by trainers to effectively educate enthusiasts, and by teachers to introduce contemporary ML topics in classrooms with minimal effort and high clarity.

  • 2 authors
·
Jan 7

From Reproduction to Replication: Evaluating Research Agents with Progressive Code Masking

Recent progress in autonomous code generation has fueled excitement around AI agents capable of accelerating scientific discovery by running experiments. However, there is currently no benchmark that evaluates whether such agents can implement scientific ideas when given varied amounts of code as a starting point, interpolating between reproduction (running code) and from-scratch replication (fully re-implementing and running code). We introduce AutoExperiment, a benchmark that evaluates AI agents' ability to implement and run machine learning experiments based on natural language descriptions in research papers. In each task, agents are given a research paper, a codebase with key functions masked out, and a command to run the experiment. The goal is to generate the missing code, execute the experiment in a sandboxed environment, and reproduce the results. AutoExperiment scales in difficulty by varying the number of missing functions n, ranging from partial reproduction to full replication. We evaluate state-of-the-art agents and find that performance degrades rapidly as n increases. Agents that can dynamically interact with the environment (e.g. to debug their code) can outperform agents in fixed "agentless" harnesses, and there exists a significant gap between single-shot and multi-trial success rates (Pass@1 vs. Pass@5), motivating verifier approaches to our benchmark. Our findings highlight critical challenges in long-horizon code generation, context retrieval, and autonomous experiment execution, establishing AutoExperiment as a new benchmark for evaluating progress in AI-driven scientific experimentation. Our data and code are open-sourced at https://github.com/j1mk1m/AutoExperiment .

  • 4 authors
·
Jun 24

Learning to Mine Aligned Code and Natural Language Pairs from Stack Overflow

For tasks like code synthesis from natural language, code retrieval, and code summarization, data-driven models have shown great promise. However, creating these models require parallel data between natural language (NL) and code with fine-grained alignments. Stack Overflow (SO) is a promising source to create such a data set: the questions are diverse and most of them have corresponding answers with high-quality code snippets. However, existing heuristic methods (e.g., pairing the title of a post with the code in the accepted answer) are limited both in their coverage and the correctness of the NL-code pairs obtained. In this paper, we propose a novel method to mine high-quality aligned data from SO using two sets of features: hand-crafted features considering the structure of the extracted snippets, and correspondence features obtained by training a probabilistic model to capture the correlation between NL and code using neural networks. These features are fed into a classifier that determines the quality of mined NL-code pairs. Experiments using Python and Java as test beds show that the proposed method greatly expands coverage and accuracy over existing mining methods, even when using only a small number of labeled examples. Further, we find that reasonable results are achieved even when training the classifier on one language and testing on another, showing promise for scaling NL-code mining to a wide variety of programming languages beyond those for which we are able to annotate data.

  • 5 authors
·
May 22, 2018

Can LLMs Generate Novel Research Ideas? A Large-Scale Human Study with 100+ NLP Researchers

Recent advancements in large language models (LLMs) have sparked optimism about their potential to accelerate scientific discovery, with a growing number of works proposing research agents that autonomously generate and validate new ideas. Despite this, no evaluations have shown that LLM systems can take the very first step of producing novel, expert-level ideas, let alone perform the entire research process. We address this by establishing an experimental design that evaluates research idea generation while controlling for confounders and performs the first head-to-head comparison between expert NLP researchers and an LLM ideation agent. By recruiting over 100 NLP researchers to write novel ideas and blind reviews of both LLM and human ideas, we obtain the first statistically significant conclusion on current LLM capabilities for research ideation: we find LLM-generated ideas are judged as more novel (p < 0.05) than human expert ideas while being judged slightly weaker on feasibility. Studying our agent baselines closely, we identify open problems in building and evaluating research agents, including failures of LLM self-evaluation and their lack of diversity in generation. Finally, we acknowledge that human judgements of novelty can be difficult, even by experts, and propose an end-to-end study design which recruits researchers to execute these ideas into full projects, enabling us to study whether these novelty and feasibility judgements result in meaningful differences in research outcome.

  • 3 authors
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Sep 6, 2024 3

Machine Learning and Deep Learning -- A review for Ecologists

1. The popularity of Machine learning (ML), Deep learning (DL), and Artificial intelligence (AI) has risen sharply in recent years. Despite this spike in popularity, the inner workings of ML and DL algorithms are often perceived as opaque, and their relationship to classical data analysis tools remains debated. 2. Although it is often assumed that ML and DL excel primarily at making predictions, ML and DL can also be used for analytical tasks traditionally addressed with statistical models. Moreover, most recent discussions and reviews on ML focus mainly on DL, missing out on synthesizing the wealth of ML algorithms with different advantages and general principles. 3. Here, we provide a comprehensive overview of the field of ML and DL, starting by summarizing its historical developments, existing algorithm families, differences to traditional statistical tools, and universal ML principles. We then discuss why and when ML and DL models excel at prediction tasks and where they could offer alternatives to traditional statistical methods for inference, highlighting current and emerging applications for ecological problems. Finally, we summarize emerging trends such as scientific and causal ML, explainable AI, and responsible AI that may significantly impact ecological data analysis in the future. 4. We conclude that ML and DL are powerful new tools for predictive modeling and data analysis. The superior performance of ML and DL algorithms compared to statistical models can be explained by their higher flexibility and automatic data-dependent complexity optimization. However, their use for causal inference is still disputed as the focus of ML and DL methods on predictions creates challenges for the interpretation of these models. Nevertheless, we expect ML and DL to become an indispensable tool in E&E, comparable to other traditional statistical tools.

  • 2 authors
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Apr 11, 2022

Scaling MLPs: A Tale of Inductive Bias

In this work we revisit the most fundamental building block in deep learning, the multi-layer perceptron (MLP), and study the limits of its performance on vision tasks. Empirical insights into MLPs are important for multiple reasons. (1) Given the recent narrative "less inductive bias is better", popularized due to transformers eclipsing convolutional models, it is natural to explore the limits of this hypothesis. To that end, MLPs offer an ideal test bed, being completely free of any inductive bias. (2) MLPs have almost exclusively been the main protagonist in the deep learning theory literature due to their mathematical simplicity, serving as a proxy to explain empirical phenomena observed for more complex architectures. Surprisingly, experimental datapoints for MLPs are very difficult to find in the literature, especially when coupled with large pre-training protocols. This discrepancy between practice and theory is worrying: Do MLPs reflect the empirical advances exhibited by practical models? Or do theorists need to rethink the role of MLPs as a proxy? We provide insights into both these aspects. We show that the performance of MLPs drastically improves with scale (93% on CIFAR10, 79% on CIFAR100, 69% on TinyImageNet), highlighting that lack of inductive bias can indeed be compensated. We observe that MLPs mimic the behaviour of their modern counterparts faithfully, with some components in the learning setting however surprisingly exhibiting stronger or unexpected behaviours. Due to their inherent computational efficiency, large pre-training experiments become more accessible for academic researchers. All of our experiments were run on a single GPU.

  • 3 authors
·
Jun 23, 2023

ArchGym: An Open-Source Gymnasium for Machine Learning Assisted Architecture Design

Machine learning is a prevalent approach to tame the complexity of design space exploration for domain-specific architectures. Using ML for design space exploration poses challenges. First, it's not straightforward to identify the suitable algorithm from an increasing pool of ML methods. Second, assessing the trade-offs between performance and sample efficiency across these methods is inconclusive. Finally, lack of a holistic framework for fair, reproducible, and objective comparison across these methods hinders progress of adopting ML-aided architecture design space exploration and impedes creating repeatable artifacts. To mitigate these challenges, we introduce ArchGym, an open-source gym and easy-to-extend framework that connects diverse search algorithms to architecture simulators. To demonstrate utility, we evaluate ArchGym across multiple vanilla and domain-specific search algorithms in designing custom memory controller, deep neural network accelerators, and custom SoC for AR/VR workloads, encompassing over 21K experiments. Results suggest that with unlimited samples, ML algorithms are equally favorable to meet user-defined target specification if hyperparameters are tuned; no solution is necessarily better than another (e.g., reinforcement learning vs. Bayesian methods). We coin the term hyperparameter lottery to describe the chance for a search algorithm to find an optimal design provided meticulously selected hyperparameters. The ease of data collection and aggregation in ArchGym facilitates research in ML-aided architecture design space exploration. As a case study, we show this advantage by developing a proxy cost model with an RMSE of 0.61% that offers a 2,000-fold reduction in simulation time. Code and data for ArchGym is available at https://bit.ly/ArchGym.

  • 11 authors
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Jun 15, 2023

The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery

One of the grand challenges of artificial general intelligence is developing agents capable of conducting scientific research and discovering new knowledge. While frontier models have already been used as aids to human scientists, e.g. for brainstorming ideas, writing code, or prediction tasks, they still conduct only a small part of the scientific process. This paper presents the first comprehensive framework for fully automatic scientific discovery, enabling frontier large language models to perform research independently and communicate their findings. We introduce The AI Scientist, which generates novel research ideas, writes code, executes experiments, visualizes results, describes its findings by writing a full scientific paper, and then runs a simulated review process for evaluation. In principle, this process can be repeated to iteratively develop ideas in an open-ended fashion, acting like the human scientific community. We demonstrate its versatility by applying it to three distinct subfields of machine learning: diffusion modeling, transformer-based language modeling, and learning dynamics. Each idea is implemented and developed into a full paper at a cost of less than $15 per paper. To evaluate the generated papers, we design and validate an automated reviewer, which we show achieves near-human performance in evaluating paper scores. The AI Scientist can produce papers that exceed the acceptance threshold at a top machine learning conference as judged by our automated reviewer. This approach signifies the beginning of a new era in scientific discovery in machine learning: bringing the transformative benefits of AI agents to the entire research process of AI itself, and taking us closer to a world where endless affordable creativity and innovation can be unleashed on the world's most challenging problems. Our code is open-sourced at https://github.com/SakanaAI/AI-Scientist

  • 6 authors
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Aug 12, 2024 10

A Comprehensive Survey of Mixture-of-Experts: Algorithms, Theory, and Applications

Artificial intelligence (AI) has achieved astonishing successes in many domains, especially with the recent breakthroughs in the development of foundational large models. These large models, leveraging their extensive training data, provide versatile solutions for a wide range of downstream tasks. However, as modern datasets become increasingly diverse and complex, the development of large AI models faces two major challenges: (1) the enormous consumption of computational resources and deployment difficulties, and (2) the difficulty in fitting heterogeneous and complex data, which limits the usability of the models. Mixture of Experts (MoE) models has recently attracted much attention in addressing these challenges, by dynamically selecting and activating the most relevant sub-models to process input data. It has been shown that MoEs can significantly improve model performance and efficiency with fewer resources, particularly excelling in handling large-scale, multimodal data. Given the tremendous potential MoE has demonstrated across various domains, it is urgent to provide a comprehensive summary of recent advancements of MoEs in many important fields. Existing surveys on MoE have their limitations, e.g., being outdated or lacking discussion on certain key areas, and we aim to address these gaps. In this paper, we first introduce the basic design of MoE, including gating functions, expert networks, routing mechanisms, training strategies, and system design. We then explore the algorithm design of MoE in important machine learning paradigms such as continual learning, meta-learning, multi-task learning, and reinforcement learning. Additionally, we summarize theoretical studies aimed at understanding MoE and review its applications in computer vision and natural language processing. Finally, we discuss promising future research directions.

  • 2 authors
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Mar 10

Paired Open-Ended Trailblazer (POET): Endlessly Generating Increasingly Complex and Diverse Learning Environments and Their Solutions

While the history of machine learning so far largely encompasses a series of problems posed by researchers and algorithms that learn their solutions, an important question is whether the problems themselves can be generated by the algorithm at the same time as they are being solved. Such a process would in effect build its own diverse and expanding curricula, and the solutions to problems at various stages would become stepping stones towards solving even more challenging problems later in the process. The Paired Open-Ended Trailblazer (POET) algorithm introduced in this paper does just that: it pairs the generation of environmental challenges and the optimization of agents to solve those challenges. It simultaneously explores many different paths through the space of possible problems and solutions and, critically, allows these stepping-stone solutions to transfer between problems if better, catalyzing innovation. The term open-ended signifies the intriguing potential for algorithms like POET to continue to create novel and increasingly complex capabilities without bound. Our results show that POET produces a diverse range of sophisticated behaviors that solve a wide range of environmental challenges, many of which cannot be solved by direct optimization alone, or even through a direct-path curriculum-building control algorithm introduced to highlight the critical role of open-endedness in solving ambitious challenges. The ability to transfer solutions from one environment to another proves essential to unlocking the full potential of the system as a whole, demonstrating the unpredictable nature of fortuitous stepping stones. We hope that POET will inspire a new push towards open-ended discovery across many domains, where algorithms like POET can blaze a trail through their interesting possible manifestations and solutions.

  • 4 authors
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Jan 7, 2019

Technical Report: Full-Stack Fine-Tuning for the Q Programming Language

Even though large language models are becoming increasingly capable, it is still unreasonable to expect them to excel at tasks that are under-represented on the Internet. Leveraging LLMs for specialized applications, particularly in niche programming languages and private domains, remains challenging and largely unsolved. In this work, we address this gap by presenting a comprehensive, open-source approach for adapting LLMs to the Q programming language, a popular tool in quantitative finance that is much less present on the Internet compared to Python, C, Java, and other ``mainstream" languages and is therefore not a strong suit of general-purpose AI models. We introduce a new Leetcode style evaluation dataset for Q, benchmark major frontier models on the dataset, then do pretraining, supervised fine tuning, and reinforcement learning to train a suite of reasoning and non-reasoning models based on the Qwen-2.5 series, spanning five parameter sizes (1.5B, 3B, 7B, 14B, 32B). Our best model achieves a pass@1 accuracy of 59 percent on our Q benchmark, surpassing the best-performing frontier model, Claude Opus-4 by 29.5 percent. Additionally, all models, even our 1.5B model, outperform GPT-4.1 on this task. In addition to releasing models, code, and data, we provide a detailed blueprint for dataset construction, model pretraining, supervised fine-tuning, and reinforcement learning. Our methodology is broadly applicable, and we discuss how these techniques can be extended to other tasks, including those where evaluation may rely on soft or subjective signals.

Reproducibility in Multiple Instance Learning: A Case For Algorithmic Unit Tests

Multiple Instance Learning (MIL) is a sub-domain of classification problems with positive and negative labels and a "bag" of inputs, where the label is positive if and only if a positive element is contained within the bag, and otherwise is negative. Training in this context requires associating the bag-wide label to instance-level information, and implicitly contains a causal assumption and asymmetry to the task (i.e., you can't swap the labels without changing the semantics). MIL problems occur in healthcare (one malignant cell indicates cancer), cyber security (one malicious executable makes an infected computer), and many other tasks. In this work, we examine five of the most prominent deep-MIL models and find that none of them respects the standard MIL assumption. They are able to learn anti-correlated instances, i.e., defaulting to "positive" labels until seeing a negative counter-example, which should not be possible for a correct MIL model. We suspect that enhancements and other works derived from these models will share the same issue. In any context in which these models are being used, this creates the potential for learning incorrect models, which creates risk of operational failure. We identify and demonstrate this problem via a proposed "algorithmic unit test", where we create synthetic datasets that can be solved by a MIL respecting model, and which clearly reveal learning that violates MIL assumptions. The five evaluated methods each fail one or more of these tests. This provides a model-agnostic way to identify violations of modeling assumptions, which we hope will be useful for future development and evaluation of MIL models.

  • 2 authors
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Oct 26, 2023